Identification of Alternative New Candidate Molecules for the Control of Apple Bract Pest by Docking Method

Nurcan Ersan Şeker; Vildan Atalay

Article Details

Identification of Alternative New Candidate Molecules for the Control of Apple Bract Pest by Docking Method

Authors:

Nurcan Ersan Şeker | Vildan Atalay

Publisher:

Süleyman Demirel University

Main Topics:

Kimya Mühendisliği (Diğer)

Journal:

Süleyman Demirel Üniversitesi Fen Bilimleri Enstitüsü Dergisi Vol.28 Issue 2, pp.260-267

Document Type:

Article

Publication Date:

8/2024

Document Language:

Turkish

Document ID (Org No.):

2001323837

pISSN:

1308-6529

Keywords:

Abstract:

 Management of the codling moth cydia pomonella pest is an issue that causes serious losses in fruit production and has become a major problem for the agricultural sector. In this study, it was aimed to determine effective and natural drug molecules in the fight against codling moth by in silico method. Within the scope of this study, using Protein Data Bank and Dr. Duke databases, 97 plant active molecules with target protein 3rvz crystal structure and insecticidal properties were selected. A study was conducted using 42 molecules that gave the best results out of 97 plant active molecules and 5 commercial insecticides. Conformer screenings, geometry optimizations, and structure-activity relationship SAR analyzes of the selected molecules were carried out with the Spartan14.V1.14 program. Autodock Tools 1.5.6 and Autodock Vina programs were used for molecular docking studies, and BIOVIA Discovery Studio Visualizer program was used to visualize the ligand-protein interaction. The results obtained were evaluated using binding affinities, linear regression plots and amino acid interaction maps. As a result of the study, candidate molecules L-7, L-9, L-13, L-14, L-16, L-18, L-19, which provide good correlation and have to be biopesticides potential, stand out. It is recommended to examine these molecules experimentally in vivo.

 Management of the codling moth cydia pomonella pest is an issue that causes serious losses in fruit production and has become a major problem for the agricultural sector. In this study, it was aimed to determine effective and natural drug molecules in the fight against codling moth by in silico method. Within the scope of this study, using Protein Data Bank and Dr. Duke databases, 97 plant active molecules with target protein 3rvz crystal structure and insecticidal properties were selected. A study was conducted using 42 molecules that gave the best results out of 97 plant active molecules and 5 commercial insecticides. Conformer screenings, geometry optimizations, and structure-activity relationship SAR analyzes of the selected molecules were carried out with the Spartan14.V1.14 program. Autodock Tools 1.5.6 and Autodock Vina programs were used for molecular docking studies, and BIOVIA Discovery Studio Visualizer program was used to visualize the ligand-protein interaction. The results obtained were evaluated using binding affinities, linear regression plots and amino acid interaction maps. As a result of the study, candidate molecules L-7, L-9, L-13, L-14, L-16, L-18, L-19, which provide good correlation and have to be biopesticides potential, stand out. It is recommended to examine these molecules experimentally in vivo.

 Management of the codling moth cydia pomonella pest is an issue that causes serious losses in fruit production and has become a major problem for the agricultural sector. In this study, it was aimed to determine effective and natural drug molecules in the fight against codling moth by in silico method. Within the scope of this study, using Protein Data Bank and Dr. Duke databases, 97 plant active molecules with target protein 3rvz crystal structure and insecticidal properties were selected. A study was conducted using 42 molecules that gave the best results out of 97 plant active molecules and 5 commercial insecticides. Conformer screenings, geometry optimizations, and structure-activity relationship SAR analyzes of the selected molecules were carried out with the Spartan14.V1.14 program. Autodock Tools 1.5.6 and Autodock Vina programs were used for molecular docking studies, and BIOVIA Discovery Studio Visualizer program was used to visualize the ligand-protein interaction. The results obtained were evaluated using binding affinities, linear regression plots and amino acid interaction maps. As a result of the study, candidate molecules L-7, L-9, L-13, L-14, L-16, L-18, L-19, which provide good correlation and have to be biopesticides potential, stand out. It is recommended to examine these molecules experimentally in vivo.

 Elma içkurdu cydia pomonella zararlısının yönetimi, meyve üretiminde ciddi kayıplara neden olan ve tarım sektörü için büyük bir sorun haline gelen bir konudur. Bu çalışmada elma içkurdu ile mücadelede in siliko yöntemiyle etkili ve doğal ilaç moleküllerin belirlenmesi hedeflenmiştir. Bu çalışma kapsamında Protein Data Bank ve Dr. Duke veri tabanlarından faydalanarak hedef protein 3rvz kristal yapısı ve insektisit özelliği olan 97 adet bitki aktif molekülleri seçilmiştir. 97 adet bitki aktif moleküllerinden en iyi sonuç veren 42 molekül ve 5 adet ticari insektisit kullanılarak bir çalışma yapılmıştır. Seçilen moleküllerin konformer taramaları, geometri optimizasyonları, yapı-aktivite ilişkisi SAR analizleri Spartan14.V1.14 programıyla gerçekleştirilmiştir. Moleküller kenetlenme çalışmalarında Autodock Tools 1.5.6 ve Autodock Vina programları kullanılmış, ayrıca ligand-protein etkileşimini görselleştirmek için BIOVIA Discovery Studio Visualizer programı kullanılmıştır. Elde edilen sonuçlar, bağlanma afiniteleri, lineer regresyon grafikleri ve aminoasit etkileşim haritaları kullanılarak değerlendirilmiştir. Yapılan çalışma sonucunda, iyi korelasyon sağlayan, biyopestisit olma potansiyeline sahip L-7, L-9, L-13, L-14, L-16, L-18, L-19 aday molekülleri öne çıkmaktadır. Bu moleküllerin in vivo deneysel olarak incelenmesi önerilmektedir.

Article Details

Identification of Alternative New Candidate Molecules for the Control of Apple Bract Pest by Docking Method

Authors:

Nurcan Ersan Şeker | Vildan Atalay

Publisher:

Süleyman Demirel University

Main Topics:

Kimya Mühendisliği (Diğer)

Journal:

Süleyman Demirel Üniversitesi Fen Bilimleri Enstitüsü Dergisi Vol.28 Issue 2, pp.260-267

Document Type:

Article

Publication Date:

8/2024

Document Language:

Turkish

Document ID (Org No.):

2001323837

pISSN:

1308-6529

Codling Moth

Insecticide

Molecular Docking

Voltage Gated Sodium ChannelsElma içkurdu

İnseksitit

Moleküler Kenetlenme

Voltaj Kapılı Sodyum Kanalları

Issues

Article Details

Authors: Nurcan Ersan Şeker | Vildan Atalay

Publisher: Süleyman Demirel University

Main Topics: Kimya Mühendisliği (Diğer)

Journal: Süleyman Demirel Üniversitesi Fen Bilimleri Enstitüsü Dergisi Vol.28 Issue 2, pp.260-267

Document Type: Article

Publication Date: 8/2024

Document Language: Turkish

Document ID (Org No.): 2001323837

pISSN: 1308-6529

Issues

Authors:

Nurcan Ersan Şeker | Vildan Atalay

Publisher:

Süleyman Demirel University

Main Topics:

Kimya Mühendisliği (Diğer)

Journal:

Süleyman Demirel Üniversitesi Fen Bilimleri Enstitüsü Dergisi Vol.28 Issue 2, pp.260-267

Document Type:

Article

Publication Date:

8/2024

Document Language:

Turkish

Document ID (Org No.):

2001323837

pISSN:

1308-6529